Tag: TRAP

TRAP 3.05 – Transcription factor Affinity Prediction

TRAP 3.05

:: DESCRIPTION

TRAP (Transcription factor Affinity Prediction) calculates the affinity of transcription factors for DNA sequences on the basis of a biophysical model. This method has proven to be useful for several applications, including for determining the putative target genes of a given factor. This protocol covers two other applications: (i) determining which transcription factors have the highest affinity in a set of sequences (illustrated with chromatin immunoprecipitation–sequencing (ChIP-seq) peaks), and (ii) finding which factor is the most affected by a regulatory single-nucleotide polymorphism.

::DEVELOPER

TRAP Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ compiler
  • R Package

:: DOWNLOAD

  TRAP

:: MORE INFORMATION

Citation

Morgane Thomas-Chollier, Andrew Hufton, Matthias Heinig, Sean O’Keeffe, Nassim El Masri, Helge G Roider, Thomas Manke and Martin Vingron.
Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs.
Nature Protocols, 3;6(12):1860-9. (2011)

TRAP 2.3 – Time-series RNA-seq Analysis Package

TRAP 2.3

:: DESCRIPTION

TRAP is a package integrating all necessary tasks such as mapping short reads, measuring gene expression levels, finding differentially expressed genes (DEGs), clustering and pathway analysis for time-series data in a single environment.

::DEVELOPER

Bio & Health Informatics Lab , Seoul National University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

TRAP

:: MORE INFORMATION

Citation

Jo K, Kwon HB, Kim S.
Time-series RNA-seq analysis package (TRAP) and its application to the analysis of rice, Oryza sativa L. ssp. Japonica, upon drought stress.
Methods. 2014 Jun 1;67(3):364-72. doi: 10.1016/j.ymeth.2014.02.001. Epub 2014 Feb 8. PMID: 24518221.

TRAP 1.1 – Tandem Repeats Analysis Program

TRAP 1.1

:: DESCRIPTION

TRAP is a Perl program that provides a unified set of analyses for the selection, classification, quantification and automated annotation of tandemly repeated sequences.

::DEVELOPER

TRAP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TRAP

:: MORE INFORMATION

Citation:

Sobreira, T.J.; Durham, A.M. & Gruber, A. (2006).
TRAP: automated classification, quantification and annotation of tandemly repeated sequences.
Bioinformatics 22(3): 361-362.

TRAP 1.1 – Tiled Regression Analysis Package

TRAP 1.1

:: DESCRIPTION

TRAP (Tiled Regression Analysis Package) is a software framework for selecting a set of genetic predictors which jointly explain trait variation with an additive regression model.. It is a package of R functions implementing the Tiled Regression analysis method.Tiled Regression (Wilson et al., 2009) is an approach to determining a regression model of trait variation when the number of possible genetic predictors is very large. It focuses initially on moderate-sized segments of the genome called “tiles” and discards those showing no evidence of significant effect on the trait. Within the more promising tiles, stepwise regression is used to select a subset of predictors that independently contribute to trait variation. Predictors that are not discarded are then combined across tiles for selection within chromosome, and then across the genome. Quantitative traits are modeled with linear regression, and binary traits are modeled with logistic regression, in each case considering only additive effects. Family relationships are handled with generalized estimating equations (GEE).

::DEVELOPER

TRAP Team @ NHGRI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows
  • R Package

:: DOWNLOAD

 TRAP

:: MORE INFORMATION

Citation:

Wilson AF, Kim Y, Sung H, Cai J, McMahon FJ, Sorant AJM,
Tiled regression: the use of regression methods in hotspot defined genomic segments to identify independent genetic variants responsible for variation in quantitative traits.
International Genetic Epidemiology Society, 18th Annual Meeting, 2009, Abstract 142